# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:49:54 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-ethyl-5-[3-(4-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(ccc2OC)c3ccccc3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 5DR  5DR  6-ethyl-5-[3-(4-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine  ligand  49  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5DR
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 5DR  N1    N  N     0  -0.489   4.8831  -0.5252  -1.5697
 5DR  C2    C  CR6   0   0.534   5.6311   0.3731  -0.9325
 5DR  N3    N  N     0  -0.475   5.3517   0.9514   0.2408
 5DR  C4    C  CR6   0   0.265   4.2118   0.6003   0.8243
 5DR  C5    C  CR6   0  -0.325   3.3410  -0.3258   0.2547
 5DR  C6    C  CR6   0   0.454   3.7424  -0.8804  -0.9906
 5DR  CAA   C  CH3   0  -0.677   2.9848   2.5043   1.8812
 5DR  CAB   C  CH3   0  -0.452  -0.4281  -3.6795  -1.8935
 5DR  NAC   N  NH2   0  -0.816   6.7708   0.7548  -1.5406
 5DR  NAD   N  NH2   0  -0.850   2.9794  -1.7880  -1.6108
 5DR  CAE   C  CSP   0   0.078   1.0481  -1.1168   1.2471
 5DR  CAF   C  CSP   0   0.132   2.1130  -0.7217   0.8377
 5DR  CAG   C  CR16  0  -0.273  -6.3716   2.8188   0.9755
 5DR  CAH   C  CR16  0  -0.221  -6.6993   1.6617   0.2804
 5DR  CAI   C  CR16  0  -0.309  -5.0561   3.0289   1.3678
 5DR  CAJ   C  CR16  0  -0.303  -5.7224   0.7228  -0.0161
 5DR  CAK   C  CR16  0  -0.225  -4.0792   2.0907   1.0683
 5DR  CAL   C  CR16  0  -0.289  -3.3701  -0.7814  -1.1421
 5DR  CAM   C  CR16  0  -0.346  -2.3920  -1.7209  -1.4387
 5DR  CAN   C  CR16  0  -0.338  -2.3278  -0.3569   0.9604
 5DR  CAO   C  CH2   0  -0.542   3.8714   1.2808   2.1161
 5DR  CAP   C  CH2   0  -0.645  -0.2587  -1.5748   1.7050
 5DR  OAS   O  O2    0  -0.453  -0.3803  -2.8654  -0.7355
 5DR  CAV   C  CR6   0   0.073  -4.3960   0.9212   0.3729
 5DR  CAW   C  CR6   0   0.085  -3.3579  -0.0787   0.0575
 5DR  CAX   C  CR6   0   0.053  -1.3439  -1.2913   0.6933
 5DR  CAZ   C  CR6   0   0.300  -1.3728  -1.9786  -0.5282
 5DR  HAA   H  HCH3  0   0.249   2.7542   2.9945   2.8262
 5DR  HAAA  H  HCH3  0   0.246   3.4814   3.2313   1.2386
 5DR  HAAB  H  HCH3  0   0.220   2.0424   2.2251   1.4110
 5DR  HAB   H  HCH3  0   0.229  -0.3590  -3.0908  -2.8110
 5DR  HABA  H  HCH3  0   0.265   0.4300  -4.3439  -1.8377
 5DR  HABB  H  HCH3  0   0.251  -1.3400  -4.2806  -1.9259
 5DR  HNAC  H  HNH2  0   0.407   7.1164   0.2120  -2.3128
 5DR  HNAA  H  HNH2  0   0.406   7.4426   1.2905  -1.0190
 5DR  HNAD  H  HNH2  0   0.382   3.2439  -2.1321  -2.5168
 5DR  HNAB  H  HNH2  0   0.399   2.0803  -2.0456  -1.2416
 5DR  HAG   H  HCR6  0   0.270  -7.1350   3.5494   1.2105
 5DR  HAH   H  HCR6  0   0.249  -7.7223   1.4829  -0.0242
 5DR  HAI   H  HCR6  0   0.227  -4.7861   3.9298   1.9033
 5DR  HAJ   H  HCR6  0   0.226  -6.0007  -0.1850  -0.5379
 5DR  HAK   H  HCR6  0   0.256  -3.0550   2.2814   1.3626
 5DR  HAL   H  HCR6  0   0.230  -4.1396  -0.5882  -1.8788
 5DR  HAM   H  HCR6  0   0.286  -2.4382  -2.2355  -2.3878
 5DR  HAN   H  HCR6  0   0.252  -2.3028   0.1565   1.9150
 5DR  HAO   H  HCH2  0   0.275   3.3610   0.5832   2.7831
 5DR  HAOA  H  HCH2  0   0.223   4.7980   1.5855   2.6055
 5DR  HAP   H  HCH2  0   0.292  -0.2158  -2.6443   1.9308
 5DR  HAPA  H  HCH2  0   0.211  -0.5047  -1.0772   2.6451

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 5DR  N1   C6    aromatic  1.328  0.020  1.328
 5DR  N1   C2    aromatic  1.331  0.020  1.331
 5DR  NAC  C2    single    1.347  0.020  1.347
 5DR  C2   N3    aromatic  1.338  0.020  1.338
 5DR  N3   C4    aromatic  1.328  0.020  1.328
 5DR  C5   C4    aromatic  1.393  0.020  1.393
 5DR  C4   CAO   single    1.499  0.020  1.499
 5DR  C6   C5    aromatic  1.421  0.020  1.421
 5DR  C5   CAF   single    1.416  0.020  1.416
 5DR  NAD  C6    single    1.338  0.020  1.338
 5DR  CAO  CAA   single    1.529  0.020  1.529
 5DR  CAA  HAA   single    0.970  0.020  1.090
 5DR  CAA  HAAA  single    0.970  0.020  1.090
 5DR  CAA  HAAB  single    0.970  0.020  1.090
 5DR  OAS  CAB   single    1.416  0.020  1.416
 5DR  CAB  HAB   single    0.970  0.020  1.090
 5DR  CAB  HABA  single    0.970  0.020  1.090
 5DR  CAB  HABB  single    0.970  0.020  1.090
 5DR  NAC  HNAC  single    0.890  0.020  1.040
 5DR  NAC  HNAA  single    0.890  0.020  1.040
 5DR  NAD  HNAD  single    0.860  0.020  1.020
 5DR  NAD  HNAB  single    0.860  0.020  1.020
 5DR  CAF  CAE   triple    1.207  0.020  1.207
 5DR  CAE  CAP   single    1.458  0.020  1.458
 5DR  CAH  CAG   aromatic  1.389  0.020  1.389
 5DR  CAG  CAI   aromatic  1.389  0.020  1.389
 5DR  CAG  HAG   single    0.930  0.020  1.080
 5DR  CAH  CAJ   aromatic  1.387  0.020  1.387
 5DR  CAH  HAH   single    0.930  0.020  1.080
 5DR  CAI  CAK   aromatic  1.387  0.020  1.387
 5DR  CAI  HAI   single    0.930  0.020  1.080
 5DR  CAJ  CAV   aromatic  1.396  0.020  1.396
 5DR  CAJ  HAJ   single    0.930  0.020  1.080
 5DR  CAV  CAK   aromatic  1.397  0.020  1.397
 5DR  CAK  HAK   single    0.930  0.020  1.080
 5DR  CAW  CAL   aromatic  1.390  0.020  1.390
 5DR  CAL  CAM   aromatic  1.388  0.020  1.388
 5DR  CAL  HAL   single    0.930  0.020  1.080
 5DR  CAZ  CAM   aromatic  1.391  0.020  1.391
 5DR  CAM  HAM   single    0.930  0.020  1.080
 5DR  CAN  CAX   aromatic  1.383  0.020  1.383
 5DR  CAN  CAW   aromatic  1.398  0.020  1.398
 5DR  CAN  HAN   single    0.930  0.020  1.080
 5DR  CAO  HAO   single    0.970  0.020  1.090
 5DR  CAO  HAOA  single    0.970  0.020  1.090
 5DR  CAP  CAX   single    1.510  0.020  1.510
 5DR  CAP  HAP   single    0.970  0.020  1.090
 5DR  CAP  HAPA  single    0.970  0.020  1.090
 5DR  CAZ  OAS   single    1.347  0.020  1.347
 5DR  CAV  CAW   single    1.475  0.020  1.475
 5DR  CAX  CAZ   aromatic  1.402  0.020  1.402

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 5DR  C6    N1   C2    117.03  3.000
 5DR  NAC   C2   N3    116.76  3.000
 5DR  N3    C2   N1    126.46  3.000
 5DR  NAC   C2   N1    116.78  3.000
 5DR  C4    N3   C2    116.77  3.000
 5DR  CAO   C4   C5    120.80  3.000
 5DR  CAO   C4   N3    116.97  3.000
 5DR  C5    C4   N3    122.20  3.000
 5DR  CAF   C5   C6    119.78  3.000
 5DR  CAF   C5   C4    124.04  3.000
 5DR  C6    C5   C4    116.18  3.000
 5DR  NAD   C6   C5    120.65  3.000
 5DR  NAD   C6   N1    117.98  3.000
 5DR  C5    C6   N1    121.37  3.000
 5DR  HAAB  CAA  HAAA  108.10  3.000
 5DR  HAAB  CAA  HAA   107.86  3.000
 5DR  HAAA  CAA  HAA   107.93  3.000
 5DR  HAAB  CAA  CAO   111.27  3.000
 5DR  HAAA  CAA  CAO   111.10  3.000
 5DR  HAA   CAA  CAO   110.46  3.000
 5DR  HABB  CAB  HABA  108.91  3.000
 5DR  HABB  CAB  HAB   108.93  3.000
 5DR  HABA  CAB  HAB   108.82  3.000
 5DR  HABB  CAB  OAS   111.63  3.000
 5DR  HABA  CAB  OAS   106.43  3.000
 5DR  HAB   CAB  OAS   112.02  3.000
 5DR  HNAA  NAC  HNAC  117.17  3.000
 5DR  HNAA  NAC  C2    118.83  3.000
 5DR  HNAC  NAC  C2    118.99  3.000
 5DR  HNAB  NAD  HNAD  118.61  3.000
 5DR  HNAB  NAD  C6    120.90  3.000
 5DR  HNAD  NAD  C6    120.01  3.000
 5DR  CAP   CAE  CAF   180.00  3.000
 5DR  CAE   CAF  C5    180.00  3.000
 5DR  HAG   CAG  CAI   120.30  3.000
 5DR  HAG   CAG  CAH   120.30  3.000
 5DR  CAI   CAG  CAH   119.39  3.000
 5DR  HAH   CAH  CAJ   119.58  3.000
 5DR  HAH   CAH  CAG   120.10  3.000
 5DR  CAJ   CAH  CAG   120.32  3.000
 5DR  HAI   CAI  CAK   119.62  3.000
 5DR  HAI   CAI  CAG   120.13  3.000
 5DR  CAK   CAI  CAG   120.25  3.000
 5DR  HAJ   CAJ  CAV   119.82  3.000
 5DR  HAJ   CAJ  CAH   119.29  3.000
 5DR  CAV   CAJ  CAH   120.88  3.000
 5DR  HAK   CAK  CAV   119.83  3.000
 5DR  HAK   CAK  CAI   119.23  3.000
 5DR  CAV   CAK  CAI   120.93  3.000
 5DR  HAL   CAL  CAW   120.21  3.000
 5DR  HAL   CAL  CAM   118.43  3.000
 5DR  CAW   CAL  CAM   121.34  3.000
 5DR  HAM   CAM  CAZ   121.20  3.000
 5DR  HAM   CAM  CAL   118.67  3.000
 5DR  CAZ   CAM  CAL   120.13  3.000
 5DR  HAN   CAN  CAX   118.27  3.000
 5DR  HAN   CAN  CAW   119.44  3.000
 5DR  CAX   CAN  CAW   122.28  3.000
 5DR  HAOA  CAO  HAO   107.54  3.000
 5DR  HAOA  CAO  CAA   109.75  3.000
 5DR  HAO   CAO  CAA   109.51  3.000
 5DR  HAOA  CAO  C4    108.68  3.000
 5DR  HAO   CAO  C4    110.03  3.000
 5DR  CAA   CAO  C4    111.25  3.000
 5DR  HAPA  CAP  HAP   106.06  3.000
 5DR  HAPA  CAP  CAX   109.23  3.000
 5DR  HAP   CAP  CAX   110.48  3.000
 5DR  HAPA  CAP  CAE   109.22  3.000
 5DR  HAP   CAP  CAE   109.67  3.000
 5DR  CAX   CAP  CAE   112.00  3.000
 5DR  CAZ   OAS  CAB   118.65  3.000
 5DR  CAW   CAV  CAK   120.94  3.000
 5DR  CAW   CAV  CAJ   120.83  3.000
 5DR  CAK   CAV  CAJ   118.23  3.000
 5DR  CAV   CAW  CAN   121.02  3.000
 5DR  CAV   CAW  CAL   121.38  3.000
 5DR  CAN   CAW  CAL   117.60  3.000
 5DR  CAZ   CAX  CAP   120.42  3.000
 5DR  CAZ   CAX  CAN   119.01  3.000
 5DR  CAP   CAX  CAN   120.57  3.000
 5DR  CAX   CAZ  OAS   116.21  3.000
 5DR  CAX   CAZ  CAM   119.65  3.000
 5DR  OAS   CAZ  CAM   124.14  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 5DR  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 5DR  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 5DR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 5DR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 5DR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 5DR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 5DR  CONST_07  CAV   CAJ  CAH  CAG     0.00   0.0  0
 5DR  CONST_08  CAV   CAK  CAI  CAG     0.00   0.0  0
 5DR  CONST_09  CAK   CAI  CAG  CAH     0.00   0.0  0
 5DR  CONST_10  CAK   CAV  CAJ  CAH     0.00   0.0  0
 5DR  CONST_11  CAW   CAV  CAJ  CAH   180.00   0.0  0
 5DR  CONST_12  CAJ   CAH  CAG  CAI     0.00   0.0  0
 5DR  CONST_13  CAJ   CAV  CAK  CAI     0.00   0.0  0
 5DR  CONST_14  CAW   CAV  CAK  CAI   180.00   0.0  0
 5DR  CONST_19  CAX   CAN  CAW  CAL     0.00   0.0  0
 5DR  CONST_20  CAX   CAZ  CAM  CAL     0.00   0.0  0
 5DR  CONST_21  CAN   CAW  CAL  CAM     0.00   0.0  0
 5DR  CONST_22  CAV   CAW  CAL  CAM   180.00   0.0  0
 5DR  CONST_23  CAN   CAX  CAZ  CAM     0.00   0.0  0
 5DR  CONST_24  CAX   CAN  CAW  CAV   180.00   0.0  0
 5DR  CONST_25  CAZ   CAM  CAL  CAW     0.00   0.0  0
 5DR  CONST_26  CAZ   CAX  CAN  CAW     0.00   0.0  0
 5DR  CONST_27  CAF   C5   C6   N1    180.00   0.0  0
 5DR  CONST_28  NAD   C6   N1   C2    180.00   0.0  0
 5DR  CONST_29  CAO   C4   N3   C2    180.00   0.0  0
 5DR  CONST_30  CAF   C5   C4   N3    180.00   0.0  0
 5DR  CONST_31  NAC   C2   N3   C4    180.00   0.0  0
 5DR  CONST_32  NAD   C6   C5   C4    180.00   0.0  0
 5DR  CONST_33  NAC   C2   N1   C6    180.00   0.0  0
 5DR  CONST_34  CAO   C4   C5   C6    180.00   0.0  0
 5DR  CONST_35  OAS   CAZ  CAM  CAL   180.00   0.0  0
 5DR  CONST_36  CAP   CAX  CAZ  CAM   180.00   0.0  0
 5DR  CONST_37  OAS   CAZ  CAX  CAN   180.00   0.0  0
 5DR  CONST_38  CAW   CAN  CAX  CAP   180.00   0.0  0
 5DR  CONST_39  HAJ   CAJ  CAH  CAG   180.00   0.0  0
 5DR  CONST_40  HAK   CAK  CAI  CAG   180.00   0.0  0
 5DR  CONST_41  HAI   CAI  CAG  CAH   180.00   0.0  0
 5DR  CONST_42  HAH   CAH  CAG  CAI   180.00   0.0  0
 5DR  CONST_43  HAG   CAG  CAH  CAJ   180.00   0.0  0
 5DR  CONST_44  HAN   CAN  CAW  CAL   180.00   0.0  0
 5DR  CONST_45  HAL   CAL  CAW  CAN   180.00   0.0  0
 5DR  CONST_46  HAM   CAM  CAL  CAW   180.00   0.0  0
 5DR  CONST_47  HNAD  NAD  C6   N1      0.00   0.0  0
 5DR  CONST_48  HNAB  NAD  C6   N1    180.00   0.0  0
 5DR  CONST_49  HNAC  NAC  C2   N1      0.00   0.0  0
 5DR  CONST_50  HNAA  NAC  C2   N1    180.00   0.0  0
 5DR  Var_01    CAA   CAO  C4   N3     93.75  30.0  2
 5DR  Var_02    CAM   CAZ  OAS  CAB    -5.91  30.0  2
 5DR  Var_03    CAN   CAX  CAP  CAE  -111.72  30.0  2
 5DR  Var_04    CAX   CAP  CAE  CAF     6.17  30.0  3
 5DR  Var_05    HAA   CAA  CAO  C4   -179.40  30.0  3
 5DR  Var_06    HAB   CAB  OAS  CAZ    63.85  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 5DR  plan-1  N1    0.020
 5DR  plan-1  C2    0.020
 5DR  plan-1  N3    0.020
 5DR  plan-1  C4    0.020
 5DR  plan-1  C5    0.020
 5DR  plan-1  C6    0.020
 5DR  plan-1  NAC   0.020
 5DR  plan-1  NAD   0.020
 5DR  plan-1  CAE   0.020
 5DR  plan-1  CAF   0.020
 5DR  plan-1  CAO   0.020
 5DR  plan-2  CAG   0.020
 5DR  plan-2  CAH   0.020
 5DR  plan-2  CAI   0.020
 5DR  plan-2  CAJ   0.020
 5DR  plan-2  CAK   0.020
 5DR  plan-2  CAV   0.020
 5DR  plan-2  CAW   0.020
 5DR  plan-2  HAG   0.020
 5DR  plan-2  HAH   0.020
 5DR  plan-2  HAI   0.020
 5DR  plan-2  HAJ   0.020
 5DR  plan-2  HAK   0.020
 5DR  plan-3  CAL   0.020
 5DR  plan-3  CAM   0.020
 5DR  plan-3  CAN   0.020
 5DR  plan-3  CAP   0.020
 5DR  plan-3  OAS   0.020
 5DR  plan-3  CAV   0.020
 5DR  plan-3  CAW   0.020
 5DR  plan-3  CAX   0.020
 5DR  plan-3  CAZ   0.020
 5DR  plan-3  HAL   0.020
 5DR  plan-3  HAM   0.020
 5DR  plan-3  HAN   0.020
 5DR  plan-4  C2    0.020
 5DR  plan-4  NAC   0.020
 5DR  plan-4  HNAC  0.020
 5DR  plan-4  HNAA  0.020
 5DR  plan-5  C6    0.020
 5DR  plan-5  NAD   0.020
 5DR  plan-5  HNAD  0.020
 5DR  plan-5  HNAB  0.020

